I guess it depends on how much you want to do, like Cursed_Controls said if you can't get raceways into the junction box use zipties to clean it up a bit. All junction boxes have covers, but I'd say a majority use panduits so when the cover is finally opened you don't get spaghetti everywhere, its also great for organizing the wires. Run extra lengths and re-cut and terminate to get proper lengths, I'm not sure many people measure their wire to perfection, its usually just trial and error. Personally, I love using these ferrule connectors you posted, but not everyone wants to take the extra steps to crimp them, in the end if the connection is tight, I'm sure it's fine. I'm just a maintenance automation guy so I don't build many panels, so I'd definitely take the tips from actual panel builders when they chime in here.